27 April 2012

Sharks! Feared ultimate predator of the sea! Striking terror into... ah, no can’t say it with a straight face when the shark in question is this:

This is the smalleye pygmy shark. It may be tiny, but it has a cool trick that few fish have.

You’ve probably noticed that the belly of fishes are lighter than their top sides. The typical explanation for this is countershading. We often see fish in tanks, with light coming in from all directions. But in water, the only source of light is above. This means the underside of the fish is in shadow. Having a lighter underside than top makes the fish blend into it surrounding, making it harder to see.

But the problem is that light varies in intensity as you go up and down in the water. It would be an advantage for a fish to be able to change how bright its underside was.

A decent number of fish are bioluminsecent, but this little shark is a bit different. Some fish, like the flashlight fish, generate a glow using bacteria. To turn the glow on and off, they cover or reveal the patch.

In this shark, the glow is generated by light generating organs called photophores. And the shark controls the brightness more directly. It’s a little bit closer to the way a cephalopod changes colour, but not as fast.

Claes and colleagues have been studying photophores in sharks for a few years now. In this new paper, they looked at how the shark controls the brightness of its photophores. It’s a neat system.

The shark switches its light “on” using a hormone: melatonin. Melatonin is a widespread chemical, and so not surprising that it would be found in these sharks.

The shark switches its light “off” using neural control: the neurotransmitter GABA will turn the light off... eventually. It’s a very slow decline, and GABA never shuts the light off entirely. The authors showed this by bath applying the GABA. Ultimately, I would like to see neural stimulation turning off the glow, but this is a good start.

I was a bit frustrated with the writing here. The story is simple, but the prose is complicated. For instance, the very first sentence starts with an exception:

Except Dalatias licha, a benthopelagic shark that can attain almost 2 m in total length (TL)...

This caveat not so important that it needs to be the first thing on the page.

A nifty finding, though. I can think of cases where a single organ has both endocrine and neural input for fast and slow changes, but I can’t think of another effector where the two opposing effects are controlled by two different organ systems off the top of my head.

25 April 2012

As a pro-research, pro-science advocacy group, I'd like to think you take facts seriously.

On your FAQ, on the very first question justifying animal research, you write:

For instance, sharks are immune to cancer. By studying their biological system, scientists hope to understand what mechanism prohibits shark cells from mutating into cancer cells, and from this information, create a medicine that mimics that mechanism to prevent cancerous cells from forming in humans and animals.

Let’s look at those two sentences in turn.

“Sharks are immune to cancer.”

This is a myth. Christie Wilcox wrote a fantastic blog post debunking this. The title says it all: “Sharks DO get cancer!” Here’s the key quote (my emphasis):

(I)n 2004, Dr Gary Ostrander and his colleagues from the University of Hawaii published a survey of the Registry for Tumors in Lower Animals. Already in collection, they found 42 tumors in Chondrichthyes species (the class of cartilaginous fish that includes sharks, skates and rays). These included at least 12 malignant tumors and tumors throughout the body. Two sharks had multiple tumors, suggesting they were genetically susceptible or exposed to extremely high levels of carcinogens. There were even tumors found in shark's cartilage! Ostrander hoped that this information would finally put to rest the myth that sharks are somehow magically cancer-free.

The second sentence claims that there are researchers who are actively studying cancer in sharks. That sharks do get cancer does not mean that there would be no researchers on them, so this is a completely separate claim. This is also not true, as far as I have been able to find.

A PubMed search for “cancer” and “shark” reveals a fifteen articles with those words in the title. None reveal any researchers using sharks to study cancer. Most of those papers bemoan the use of shark cartilage as quackery, and a few test the shark cartilage treatment (it failed). Another search for “tumor” and “shark” finds a few papers that are testing shark derived products on cancer. But testing a shark product for anti-cancer properties is not the same as studying sharks.

I can find nobody doing the type of research you describe in your answer: studying the cellular biology of sharks. I may be wrong on this, and would like to knowing what researchers are actively studying tumorigenesis in sharks.

The combination of these two claims may give people the false impression that there is something the quack science concerning treatment of cancers using shark cartilage. This is also not true, and contributes to severe overfishing of sharks (also addressed in Christie Wilcox’s post).

Beside, using sharks as an example misses the point that concerns most people. Most people are concerned about the use of mammals in research. You should address that directly and use mammals in answering the question.

One alternative would be to naked mole rats in the example. There is ongoing research on tumorigenesis in this species; references are below. Frankly, an example of information gained from a more common lab animal, like a mouse, would be even more convincing.

I hope you will consider changing your FAQ. As a researcher, I am very concerned about issues surrounding animal care. Errors like this can damage the credibility of everyone who has to use animals in research.

Yours truly,

Zen Faulkes

Additional: I emailed this to AMP this morning, and received an email back from them in about five hours. They plan on reviewing their FAQ and should have a revised version up soon.

Hooray!

Update, 26 November 2013: I had cause to revisit this post because David Shiffman tweeted a new picture of a shark with a tumour from this scientific paper. I hopped over to the Americans for Medical Progress FAQ, and saw (my emphasis):

The differences exhibited in a research model can also provide great
insights. For instance, sharks rarely get cancer, cockroaches can
regenerate damaged nerves, and some amphibians can regrow lost limbs.

This is not a great revision. It still perpetuates the idea that somehow sharks are at least resistant to cancer, and that there is active research on this. Many other species have low rates of cancer, like whales, crustaceans, and naked mole rats. Naked mole rats probably have the most research on their inherent cancer resistance.

I was particularly interested in this “denial manual,” discussed by Sean B. Carroll in the former conference. It was taken from chiropractic attacks on vaccines, but you can see the exact same playbook at work in evolution, global warming, and so on.

And, as if to demonstrate, a few climate change denialists found the #sciencedenial and #denialconf hashtags on Twitter. Among the first words they typed were accusations of some of those at the conference being liars and idiots – neatly showing how Point #2 above works.

Similarly, one hashtag got flooded with automated porn spambots. The switch to a second hashtag was seen as evidence of those at the conference not wanting to listen to arguments and “paranoia,” rather than not wanting to wade through irrelevant, automated tweets linking to pornography.

To get a glimpse of Point #5 in action, have a listen to Marc Morano on The Science Show. Morano says to Anna Rose (co-founder of the Australian Youth Climate Coalition):

You are the face of one of the greatest threats of our liberty, and that is intellectual, international bean-counters trying to control average people's lives because they think they know better how people should live, because people left to their own devices will somehow destroy the planet.

If you don't want to listen to Morano, you should listen to Ben Goldacre later in the clip, who has a memorable description of how frustrated he is with the climate debate.

A Storify of the first part of the Science Denial meeting can be found here and here.

Additional: Interesting. The Twitter stream for #denialconf was subject to another attack by porn bots today, at about the same time of day as yesterday. It certainly looks like a deliberate attack on the conference stream, not just happenstance.

As for whether yesterday’s switch to a new hashtag was refusal to engage, here’s a screen grab from today to give an idea of the level of tweets that led to the switch. Click to enlarge.

23 April 2012

This is mostly going to be a link round-up for reviews and news related to The Revisionaries movie. I’ll update it I find more review.

23 April 2012

IndieWire blog: “Director Scott Thurman always seems to let the right bit of footage speak for itself in these situations: opposition to the teaching of the Enlightenment and Thomas Jefferson’s placement in the textbook are explained by a representative who prefaces her opinions by saying, ‘I love Jefferson, I'm a huge fan.’ The Apostle Of Democracy, reduced to mascot.”

The Wrap blog: “Thurman never turns his film into an advocacy doc the way the way he easily could have done, but he has produced a frightening look at the politicalization of education, and at an arena too often dominated by what one SMU scientist calls ‘a flammable mixture of ignorance and arrogance.’”

PoliTex blog: “(Cynthia) Dunbar (former Texas State Board of Education member - ZF) said even though “experts” oppose discussing other views as science, “that’s what they talked about in pre-Holocaust Germany as well.’ ... Thurman, 31, wept when he talked about McLeroy, calling him a ‘warm and kind’ man who cooperated completely.”

Don McLeroy (also former State Board of Education member) is going to be a guest on The Colbert Report tonight, ostensibly to talk about the film. I’m willing to bet there won’t be so much about the film as McLeroy’s religious beliefs.

Additional: Here’s a link to McLeroy on The Colbert Report. As usual, Colbert gets in a good quips: “I believe science can be a personal choice,” and “I have always been a fan of reality by majority vote.”

"The Revisionaries" doesn’t preach, but it doesn’t need to in order to make its major point.

Thurman bends over backward to maintain something resembling objectivity, and religious belief is never ridiculed. ...

Production values are tops, particularly the lensing by Thurman and Zac Sprague, capturing not only the colorful debate on the board but the often bewildered reactions elsewhere. Jawad Metni's editing is also tops.

Defenders of biological sciences can also fall back on court rulings such as Kitzmiller v Dover Area School District and Edwards v Aguillard, which prohibit teaching of creationism. They also have a wealth of popular treatments of scientific issues to draw upon, such as explanations of evolutionary theory by Richard Dawkins and other scientists.

History, however, is often left to fend for itself.

21 June 2012: Public radio station WBUR has an interview with the producer of The Revisionaries, Vijay Dewan, and Don McLeroy. I always appreciate McLeroy’s honesty in admitting the harm those standards do to teaching evolution (my emphasis):

The science magazine, you know, the American Association for the Advancement of Science reported after we passed the standards that new science standards for Texas schools strike a major blow to the teaching of evolution. And really, they're right because what they do is, when they highlight these weaknesses, now the textbooks have to explain these weaknesses.

Of course he’s a nut case. ... But here’s the deal: when interviewed on Talk of the Nation, his host, Neal Conan, didn’t challenge any of the fundamentals of his presentation. Nor did the documentary’s executive producer, Vijay Dewan, who is, for promotional purposes, temporarily joined at the hip to McLeroy.

To a point, Thurman does an admirable job portraying McLeroy with some objectivity. The director’s stated goal is to allow us to appreciate the “compassion and complexities of Don’s character,” but by the end of the film, the tenor of Thurman’s coverage shifts perceptibly into the unsympathetic. Granted, there isn’t an easy way to portray certain statements of McLeroy’s in a favorable light. Example: “Somebody's got to stand up to the experts.”

One of the great things about Scott Thurman’s film — a low-budget but thoroughly watchable documentary, largely funded on Kickstarter – is that it helped me see the world from McLeroy’s point of view, which I might previously have considered impossible.

I think this is my favourite review of the movie to date; it’s very well-written.

Interviewing a wide range of concerned parties, Mr. Thurman’s presentation is admirably evenhanded; though he clearly supports the scientists, for example, he avoids the temptation to ridicule the commissioners. Instead, they open up and explain their perspectives.

And the Houston Chronicle reports on a screening and mentions the Times review.

The film director sees his work as a mixture “of medicine and sugar.” Thurman reminded his audience that making a documentary film about the board of education is inherently difficult. It’s important (the medicine part of the story) but sometimes weighty and dry

Additional, 27 January 2013: Reviews are starting up again in anticipation of the showing of The Revisionaries on PBS next week. This one is at Ars Technica:

Enough people describe the whole process as a mess that it’s no surprise The Revisionaries struggles to lay it out in a narrative. The challenge is made larger by the filmmakers' decision to provide little framing for the footage, other than sporadic notes scratched on a blackboard to give some sense of the timing and location of the clips. As a result, the movie really doesn't work if you go into it hoping to get a history of the Texas school board. In fact, it would probably be better if you went in to things with a rough outline of the events (the one in this review would be enough).

But if you've got that, the film is a fascinating glimpse into the sorts of thinking that drive the public controversies that have happened in Texas and elsewhere.

Last week, I wrote about women and red. To recap: Men think that women wearing red look smokin’ hawt. (That’s the technical term.)

There’s a lot of questions you can ask about that fact. Last week's paper tried to figure out if red was sexy because it reminded men of the colour of female sex organs. (No.) Another question, tested here, is whether women use red to show their interest in sex.

This new paper by Elliot and Pazda has some similarities to the hypothesis of the previous paper. The authors imply that red is a sexual signal because of biology more than culture. The paper's first sentence is:

Females in many primate species, such as baboons and chimpanzees, display red on their body (e.g., chest, genitalia) near ovulation.

(Because of lead time, Elliot and Pazda don’t mention the paper from last week. They couldn't have known that the “red makes men think of women’s sex organs” hypothesis was not supported.)

The authors did three studies, all online. But I am frustrated by a lot of missing details. The authors mention their own website, and other existing “dating websites,” and we aren’t told anything else about them.

See, here's the thing. The Internet? It's a big place. (I live in Texas. “Big” is kind of a local obsession.) If you want to argue that the effects you’re seeing are biological rather than cultural, we need to know something about the particular websites used. What was the primary language of the website, for instance? I’m almost willing to bet that these were English language sites based in the United States.

That sort of detail could make a big difference in the strength of the interpretation. It’s hard to rule out or control for confounding factors, particularly good old culture (as Sci notes). This research would be much stronger if it had a cross-cultural component. For instance, in China, red is associated with good fortune... and I don’t mean “getting lucky.” Elliot and Pazda do note that they had a mix of ethnic groups in their first experiment, but not their nation of origin.

In the first experiment, they asked women hypothetically what they would show in a profile pic on a dating website, and varied the instructions as to whether there is a mention of casual sex or not. When casual sex was mentioned, “red” was the most popular colour chosen by women, and it was was a significantly more common choice than when casual sex was not mentioned. Blue was the most common colour when casual sex wasn’t mentioned.

Things get more complicated on the existing, functioning dating websites. On these websites, most women were wearing black – more than red and blue and green combined. Those women who indicated an interest in casual sex were more likely to be wearing red in their picture, which is consistent with the hypothesis. But the popularity of black doesn’t make for a straightforward interpretation.

Maybe these were dating sites for goths?

We just don’t know!

In the discussion, Eliot and Pazda do add nuance. They still seem to favour a biological interpretation of their results, with some references to primate literature. They admit, however, that they can’t rule out the cultural explanations. They also talk about whether red is simply a signal to men, or whether it is also intended as a signal to other women (that is, potential competitors).

I do find it odd that this paper frames its discussion from a heterosexual perspective. There is no speculating on whether red would be used by people of other orientations in the same way. This seems a curious omission, because Elliot and Pazda mention that their first two studies contained women who identified themselves as bisexual.

Maybe I’ve been spoiled. Frankly, OK Cupid did this kind of stuff better. Their OKTrends blog posts were often much more detailed and rich than this paper, and I’d love to have seen them tackle this question. I imagine they wouldn’t just have data on what the women wore, but they’d have data on how often men responded to those profile pics where women wore red. And how gay women responded to pics with red. And bi women. And so on.

17 April 2012

I recently described myself as a “crustacean biologist” for a project I was working on. But whenever I do, I feel like such a sham, because I barely have a clue about critters like these...

I look at these and have a hard time believing that some of these are even animals.

These are examples of tanaidaceans. Haven’t heard of them? Don’t worry. I was at best only vaguely aware of their existence, too.

A recent paper by Blazewicz-Paszkowycz and colleagues is a nice little introduction to this little known group. They are almost all small burrowing animals living in sediment. They have almost zero ability to disperse, and so they become isolated and for mew species frequently as they become isolated. There are about 1,200 species known, but the rate of discovery has consistently increased. The authors estimate that for every known tanadacean species, there may be nine undescribed ones awaiting discovery.

16 April 2012

As a professor, I'm expected to excel at a lot of tasks, each one of which can be a full-time job of its own.

For instance, researcher are expected to master techniques to gather data. But then there's the statistical analysis, creation of charts, and writing it all up.

With teaching, the skill set required here is expanding, too, with the increase of online teaching. Lecturing and online are rather different skill sets.

Both teaching and research require presentation skills. And I daresay the standards may well be increasing.

I've read a lot of people who talk about the desire to have had more training in management of a lab: inventory, accounting, personnel management, project management. I certainly felt the difference between being a postdoctoral research

With the second round of SciFund, I found myself working to make YouTube videos. Now I need to understand storytelling, editing, and sound mixing.

The ever-increasing power of computers has opened up the ability for a single person to do more of these tasks. Going digital has put what was once expensive tools of pros into the hands of many more people, like video editing. And it's easy to make the mistake that because those tools are fairly readily available, that everyone should learn to use them. I'm guilty of this myself, advocating that people learn how to use a dedicated graphics program.

13 April 2012

The other day, Jacquelyn Gill mentioned that she found herself swearing more as the defense date for her dissertation drew closer. This struck me as pretty mild. Hey, we're all adults in higher education.

But I got thinking about social gaffes and decisions that are now most often called, "inappropriate."

It was a seminar, of the sort than many departments have. An hour long research presentation attended by students and post-docs and faculty. It was on some advances related to DNA analysis.

As the speaker was going along, he was making some point about discovery or analysis. He started with a black screen, and then revealed part of what was behind it. It was a boat on a beach.

This continued, and soon the image showed that there is an attractive woman standing next to boat. But, like the rest of the image, we don't see all of her at once. And, because it was on a beach, it became plain as more black squares fade away that she is wearing a swimsuit.

As the speaker continued to make points about uncovering new information, this continued, until there was only one last black square on the picture. Across the model's chest.

I was sitting there thinking, "He wouldn't."

He did.

The last square vanished, revealing that the model was topless.

The room was extremely quiet. I'm not sure if he was expecting a different reaction, but after a moment, perhaps sensing the mood in the room, the presenter said, "I didn't mean to offend anyone." And he carried on from there.

Nobody mentioned it the questions, either. I think all the audience members were acutely embarrassed.

I never was quite able to figure out why he felt that including a strip tease slide in a presentation at a biology department in a major research university would be a good idea. The science was actually interesting, and stood on its own without the cheesecake.

But it certainly did give me good fodder for the year in review at the annual department Christmas party.

I was particularly glad to be able to use this quote from August Krogh, who is best known for advocating the choice of lab animals based on experimental convenience. But Krogh was no mere pragmatist, and found delight in organisms as they were:

You will find in the lower animals mechanisms and adaptations of exquisite beauty and the most surprising character.

11 April 2012

The prisoner’s dilemma is a classic problem of cooperation. You’ll find lengthy and erudite academic discussions of it in many fields of academia, from evolution to behavioural economics.

I wouldn’t have pegged it as a staple for a television game show.

Golden Balls is a UK game show that always ends with a prisoner’s dilemma decision. Burton-Chellew and West took advantage of this to study the prisoner’s dilemma respond “in the wild.”

Golden Balls goes through several rounds; I have a whole episode in links below. Early rounds give players ample reason and opportunity to lie. The penultimate “test your psychic powers” segment has players randomly selecting balls, which determines the final total they will play for in the end. In the final round, two players are left, and they have to make a decision: split or steal?

Both players make independent decisions. If they both choose “split,” they the pot of money is split 50-50%. If one chooses “Steal,” that player gets all the money (twice what they’d get by splitting) and the other gets nothing. But if both pick “steal,” neither gets anything.

Here is an example of a final, high stakes decision, for “life-changing” money (as the presenter is fond of calling it):

Not all the stakes are quite so high, though:

By watching every episode of the show on DVD, Burton-Chellew and West found there was no overall pattern to splitting or stealing; it was almost exactly split down the middle. This was a bit of a surprise to me, as I’d understood that people tended to cooperate more.

Lots of factors were correlated with the decision, but one of the biggest ones was the amount of money at stake. With more money at stake, contestants were more likely to steal. People got greedy.

The earlier rounds, where players often had to lie, did affect the decisions of the contestants. There were hints of retribution. Lies about the amount of cash the player had made their opponent more likely to steal.

There are few cases where a player will admit to planning to steal the jackpot. Were there ways to tell who was being honest? One signal that seemed to be an honest signal was laughter. Another was reciprocal physical contact. But if only one player touched the other... it was more likely there would be stealing. Sadly, although both of these seemed to be somewhat honest signals, there was very little evidence that players picked up on these reasonably reliable cues from their opposite number!

One limitation of this study is that game show contestants are hardly selected at random. The producers may well have screened their contestants to get both strategies about equally represented in the game. This makes some of the other demographic information (i.e., that women split more) problematic. The authors address the non-random selection, but they focus more on the possibility of certain personalities wanting to be on TV, more than active choices by producers.

Further, game shows are a very strange situation. People may be inclined to think, “What happens on the game show, stays on the game show.”

Still, if you’re wondering if you can trust someone, asking yourself if whether he or she makes you laugh might be a good first question to ask.

09 April 2012

The Methods section of most papers is the least read part of the paper. You can see this in how some journals print the Methods in a tiny point size. Others have taken to putting the section at the end of the paper, so as not to disrupt the narrative flow with details.

Occasionally, you get a paper – usually in your field – where you need to read the Methods section closely to understand a paper enough to criticize or replicate.

Rare indeed are papers where the story is so unusual that I think, “I have absolutely got to read that Methods section!”

A new paper by Johns and colleague marks the first time I thought, “I have to read those Methods,” and “These Methods should come with an NSFW warning.”

It’s about the colour red.

Red seems to affect us in a way that other colours don’t (Elliot et al. 2007, Hill & Barton 2005). Case in point:

These head-turning dresses would not be the show-stoppers they are if they were beige.

Red is sexy.

If that picture doesn’t convincing you, check out Elliot and Niesta, 2008 and go through the data to your heart’s content.

Johns and colleagues test an hypothesis for why red on women looks so attractive to me. The hypothesis is that red is sexy because it reminds men of... lady parts.

An obvious objection to this idea is that t external sex organs of women are not red in the way that the dresses above are red. The hypothesis is a more subtle, however. One version of the hypothesis is that as females are approaching ovulation, the vulva becomes more red than is is at other points in the cycle.

If this “red is code for female sex organs” hypothesis is true, you might predict that men would judge female genitals as more attractive as they became more red.

The Methods section does not disappoint.

Explicit images of anatomically normal, un-retouched, nonpornographic, similarly-orientated female genitals were surprisingly difficult to obtain... We selected photographs that ... did not contain other, potentially distracting, objects (fingers, sex toys, piercings etc.) and were hairless to account for current fashion.

They showed their pictures to 40 males. Most of the men were in their 20s, and they asked the participants about factors like their sexual orientation (they all reported themselves to be straight) and number of sexual partners. The men rated the attractiveness of each image.

The ratings of attractiveness were the exact opposite of those predicted by the signalling hypothesis. The reddest images were rated the least attractive.

The authors are then tasked to come up with an hypothesis as to why redness is less attractive. Their suggestion is that red is suggestive of menstrual blood. I'm not sure how one would test this hypothesis.

The results also showed that there was no difference in the judgments of men depending on their sexual experience. I learned from the Methods section of this paper that... shhhh, don’t spread this around... one can find pictures of female genitalia on the Internet. Is is possible that the men in this study knew this and might have looked at pictures of ladybits before participating in the study? I know, it’s incredibly unlikely, am I right? But if they did, it might explain why they found no difference in attractiveness ratings according to number of partners the men had.

This study is useful in that it tries to test an adaptive hypothesis experimentally. But it is frustrating because it is a limited study and hard to interpret.

First, there were few stimuli used. Only four pictures were used (then coloured four shades of red, for a total of 16).

Second, and more importantly, for an hypothesis that is all about sex, the authors seemed determined to make everything as clinical and detached and, well, unsexy as possible. First, the pictures were substantially cropped. They didn’t show the labia minora or the clitoris. (Correction; see comments.) As mentioned in the quote above, they didn’t want to use images had any sort of sexual nature (non-pornographic). The female equivalent of this task might have been to evaluate penises for attractiveness from pictures that only showed a flaccid member.

Perhaps not surprisingly, the men didn’t find images of lady parts alone to be very attractive. On a scale of 1 to 100, the average was around 40, except for the reddest, which was rated 35.

I’m curious as to whether the authors would expect to see the same effect with homosexual women.

Finally, there is a great opportunity for further research. The authors note:

Surprisingly little is known about the range of variation in morphology and colour of the external genitalia of normal women of reproductive age, however, and further research is necessary in this area.

I think this could be the chance for someone (not me) to create the best citizen science project ever. “Ladies, all you need to contribute to science is privacy and a camera.” We need data!

06 April 2012

Columbia University hosted a debate between Tony Movshon and Sebastian Seung last Monday, “Does the brain’s wiring make us who we are?” This became known informally as “brainbrawl.” I watched it livestreamed through the Radiolab site, and someone had the wherewithal to grab the video below (which Radiolab said they weren’t planning on archiving). Radiolab did archive the live chat here.

Where’s the fight?

As I predicted, it was a much more sedate affair than the “brainbrawl” moniker suggested. Seung set the tone in his first comments by pulling back from the big claims that he has made previously. Instead of discussing the nature of human identity (his TED talk) or immortality (his book), he was much more circumspect in outlining what a connectome could do for us. Near the end, he said, “All I want to do is map some connections!”

I liked this, actually. It is a far more sensible view of the promise of connectomes than we’ve sometimes seen. But yes, it would have been more fun if Seung had swung for the fences anf salked about uploading consciousness. At the end, co-moderator Robert Krulwich was apologizing for the lack of blood on the floor and the modesty of the speakers.

The fight (to the extent that there is a fight), then, is not about whether connectome research is feasible or useful, but about grand challenges and resources. Movshon nailed it when he said people are looking for “gigascience” projects, and that neuroscience has been a “cottage industry.” While nobody said it directly, “gigascience” is often about making a sales pitch. People want to be at the forefront of establishing big projects, because the prospect of money is there. Someone made a comment about keeping score, and Movshon said, “The NIH is.” Krulwich asked Movshon, “What’s your recruiting pitch? What do you tell the young mavericks to bring them into the field?” (Krulwich occasionally seems to confuse science with the Wild West; also here.)

It seems to me like Seung talks about connectomes as a way to pitch his research, which involves developing techniques to do high-throughput neuroanatomy (e.g., Jain et al. 2010; he talks about this more in this interview with Jennifer Oulette). Faster, more automated electron microscopy would be a godsend. But I doubt Columbia UNiversity would have hosted a debate on, “Should we develop better EM?” One commenter on Twitter said:

I haven't heard alternatives to connectome that generate comparable ideas/excitement

I’m not sure we need it. It’s not as though neuroscience is suffering for people; remember, we hold the biggest scientific meeting in the world. personally am unconvinced that we need grand challenges in science. The history of science shows that the way you answer the big questions is by answering the small questions.

The invertebrate in the vertebrate brain

Invertebrates came up in the discussion a couple of times. Good circuit descriptions of the mammalian retina are actually fairly far along, and may be the first part of the brain for which we have a connectome. Seung commented, however, that the retina was like an invertebrate brain contained within a vertebrate brain. I think he was referring to several of the retinal cells being non-spiking, which is also true of the worm Caenorhabditis elegans.

On Twitter, Noah Gray said he didn’t think C. elegans informed the connectome debate at all, because it has non-spiking neurons. I disagree, but at the very least, it does point out the importance of the intrinsic properties of neurons. Movshon suggested that the reason that C. elegans had non-spiking neurons was that it was small. This is too simple an explanation. In crustaceans, you can find both spiking and non-spiking proprioceptive sensory neurons (e.g., Paul and Wilson, 1994), and there seems to be no readily apparent functional reason to favour one or the other.

As I’ve mentioned before, we have a connectome of C. elegans, and there was discussion about how useful it actually it. In his book, Seung admitted that the connectome hadn’t solved all the neurobiological research problems for that animal, but that it might be a special case. Seung tried to argue that C. elegans posed technical problems in recording from the neurons, but Carl Zimmer pointed out that if his hypothesis was true, that wouldn’t matter. I do think the moderators, and possibly Movshon, were too dismissive of what we have learned from the connectome of C. elegans. Seung is correct that the connectome is very important to guiding research in the nervous system of the animal.

What occurred to me, though, was that there might be another invertebrate example that shows the usefulness of determining neuronal circuits: the eye of the horseshoe crab.

Haldan K. Hartline won the Nobel prize for his work on horseshoe crab vision. Hartline was able to map connections between the photoreceptors in the crab’s eye. He had the advantages that the photoreceptors were spiking neurons (unlike in mammals), and that there was only one type of photoreceptor. That is, each was an interchangeable widget, and the properties of the neuron were largely determined by connections with other neurons. By figuring out the simple circuit in the eye, he showed how lateral inhibition was able to enhance contrast of edges. This is important because the horseshoe crab eye has very low resolution.

Many years later, Robert Barlow and colleagues used a connectome-like model to build a biologically realistic model of the horseshoe crab retina and the signal it sends to the brain (Passaglia et al. 1997; Barlow et al 2001). When it was published, it was the largest biologically realistic model that had been built. They showed that some previously puzzling features of the synapses, like neurons inhibiting themselves, did things like filter out flicker in the environment.

If the mammalian retina is an invertebrate nervous system trapped in a vertebrate brain, the horseshoe crab retina may be a vertebrate nervous system in an invertebrate brain.

Other tidbits

I liked Movshon’s comment that the brain is not a multi-purpose computer, but a specific purpose computer. That is, brains are the products of natural selection and need to do specific things very well. This contrasted with his earlier argument against studying connectomes by using a well-worm software analogy, used my many cognitive pyschologists: "Studying the hardware doesn’t tell you anything about the software.” True for your desktop computer, but the brain is not an electronic computer, as Seung noted.

The audience asked some very smart questions. I wished they’d had a chance to ask more.

Passaglia C, Dodge F, Herzog E, Jackson S, Barlow R. 1997. Deciphering a neural code for vision Proceedings of the National Academy of Sciences of the United States of America94(23): 12649-12654. PMID: 9356504

05 April 2012

A student organization asked in a medical professional to come give a talk this week.

During this talk, this physician told the students that some their professors had “a chip on their shoulder” because couldn’t get into medical school, and took it out on students by refusing to give them As.

That ticked me off a little.

I have chips aplenty on my shoulder. But none are because I wanted to get into med school and couldn’t. I don’t know of any professor who was a failed med student.

But my post will be the best, for I shall cite peer-reviewed data in the primary literature.

As it happened, Petersen and colleague published a paper yesterday looking at career success in physics. Appropriately enough, even though it’s a career paper, it feels very much like a physics paper: lots of equations and models and phrase like “leptokurtic but remarkably symmetric.” Hoooookay...

The authors tracked 300 physicists through about 20 years of their careers. They fell into three groups: phsyicists who were eminent (h -index of 61); productive and highly cited (h-index of 44), and early career assistant professors (h-index of 15). In that data from real scientists, Petersen and colleagues see that there are time when physicists are “shocked.” The shocks can be positive (“Wow, I just made this totally great discovery by accident!”) or negative (“Uh oh, they found that paper where I manipulated data.”)

They also look at career productivity, and the ability of researchers to build collaborations.That’s the “ground truth” that Petersen and colleagues use to create models of research career trajectories. This lets them play with some of the parameters.

The models indicate that as competition increases, many people can be taken out of the career pathway by... blind, stinking, clueless, doo-da luck.

Those that survive the field of bullets reach a point where they can start generating collaborative networks, and that builds even more success.

But the competition turns out to be very important in this model; and that relates to tenure. Many people want to see tenure replaced with a series of recurring short-term contracts. The authors imply that the short-term model could be harmful for the development of science. A failure in one short-term contract could derail a productive researcher, since early career shocks can ripple throughout a scientist’s career.

I think Petersen and colleagues would say that you do not have to be exceptional to make it in science. More important is the ability to tough out the early weeding out period, which doesn’t necessarily have a lot to do with your talent.

Reference

Petersen A, Riccaboni M, Stanley H, Pammolli F. 2012. Persistence and uncertainty in the academic career Proceedings of the National Academy of Sciences109(14): 5213-5218. DOI: 10.1073/pnas.1121429109

03 April 2012

This is going to be the crustacean story in the news all this week for sure...

It’s a hermit crab. His name is Harry. His is wearing a Lego shell, which is not surprising, given that he lives in an aquarium in a UK amusement park - Legoland.

This is from a Guardian story here. This picture doesn’t do justice to the accompanying video (can’t embed it, so if you want to see it, you’ll have to hit the Guardian’s website).

The article implies that the crab chose this shell over more regular snail shells. The story doesn’t make clear that the shell is not entirely Lego. In this preview image on the video (which is often partly covered by the “Play” or “Replay” icon), you can clearly see the molluscan shell that the Lego shell is built onto:

02 April 2012

Recently, I wrote a post discussing connectomes. (Recap: Connectomes are descriptions of every synaptic connection between neurons in a brain.) In it, I referred to a paper by Cornelia Bargmann and argued that the amount of enlightenment we will gain about ourselves through connectomes is being oversold. I used several quotes from Sebastian Seung as examples, and mentioned his book on the subject.

Sebastian Seung noted that I had not read his book. Fair enough. I was not trying to single out Seung, but I can see that my post uses his examples enough that it seems like I am reviewing the book without reading the book.

I bought the book and read it.

The timing has turned out to be good, for today, Carl Zimmer and Robert Krulwich are moderating a debate between Seung and Anthony Movshon at Columbia University. The formal title of this debate is, “Does the brain’s wiring make us who we are?”

The Twitter hashtag? #brainbrawl. Much more fun, although I worry it promises more sparks than one will probably get from an academic debate about neuroscience. For example, The description of the #brainbrawl debate ends with the question, “Are brain maps the future of neuroscience or an empty promise?” I doubt anyone will argue that describing connectomes will yield nothing. As I said, even though I think the enterprise will fail, on some level, it will fail in an interesting and productive way.

This book proposes a simple theory: Minds differ because connectomes differ.

I read through, making notes, and was caught off guard in the last chapter. After spending all this time making arguments for his connectome theory, I was surprised that in the last chapter, Seung surrenders the war.

Yet Seung remains optimistic that he can win one battle.

In Chapter 4, Seung argues that the function of a neuron is determined primarily by its connections with other neurons. Take a neuron from one region of the brain, stick in into another part of the brain, hook up the input and output synapses the right way, and away you go.

To put it another way, Seung initially treats neurons as interchangeable widgets.

At this point, I was getting ready to start a big long list of reasons why neurons are not interchangeable. There are not only neurons that generate action potentials, there are neurons with graded potentials, pacemaker potentials, and plateau potentials. There are the passive electrical properties of the dendritic tree. These are just a couple of examples of the long list of intrinsic properties of neurons that make them distinguishable by far more than their connections to other neurons.

These are all in addition to changes of neuronal physiology introduced by neuromodulation.

Seung addresses the intrinsic properties of neurons in the book’s last chapter:

In principle, every neuron is unique in its behavior, owing to the unique configuration of its ion channels. This is a far cry from the weighted voting model, according to which all neurons are essentially the same. But it sounds like bad news for brain simulation. If neurons were infinitely diverse, how could we ever succeed at modeling them? Measuring the properties of one neuron would tell you nothing about another.

There is one hope for escaping the morass of infinite variation: neuron types.

The concept of neuron “types” is initially introduced in Chapter 10. Seung initially wants to categorize the neurons by their connections.

If two neurons are connected to similar or analogous partners, they should be grouped in the same type.

Seung then makes an extrapolation that is plausible, but I would say not yet proven: neurons with similar anatomical connections will have similar physiology and other intrinsic properties.

(N)eurons of the same type generally exhibit the same electrical behaviors. This is presumably because their ion channels are distributed in the same way. If this is the case, then neural diversity is actually finite.

By this point in the book, Seung has already introduced the only complete connectome of any animal, that of the 302 cell nervous system of the worm, Caenorhabditis elegans. I expected that this would be used as the flagship case of how connectomes can help us understand behaviour.

Instead, Seung declares defeat.

He estimates that of the 302 neurons in C. elegans, there are about 100 different types of neurons. And that proportion of distinct neuronal types, he says, is too high for a purely connection-based model to explain the worm’s behavior.

As you read this section (emphasized sections are mine), recall that he's been repeated the mantra, “You are your connectome,” for the previous 14 chapters. Now, in the very last chapter, an important missing piece gets added.

Thus the earlier claim should be revised to say, “You are your connectome plus models of neuron types.” (Let’s assume that a connectome is defined to specify the type of each neuron.) But the models of neuron types are likely to contain much less information than the connectome, as most scientists agree that there are far fewer neuron types than neurons. In this sense, “You are your connectome” would remain a very good approximation.

So “You are your connectome” would be a terrible approximation for a worm, even though it might be almost perfect for us.

If Seung is not convinced that the connectome theory yields meaningful information for C. elegans, I am skeptical that the ratio of neuronal types to the total number of neurons in a human brain* is going to be more favourable to connectomes explaining the mind.

At the very least, we have to acknowledge that there is a continuum.

One one end, we have circuits in which activity is dominated by few types of neurons, in which understanding the synaptic connections explains a large proportion of the function. Escape circuits are excellent examples, such as those in crayfish and fishes.

On the other end, we have circuits that are composed of many personalities, and where the intrinsic physiological state of the neuron matters a great deal to the function. Seung suggests C. elegans falls into this category, and I’ll suggest the crustacean stomatogastric nervous system as another.

It is not clear to me where regions of human brains may fall on this continuum. When I visited the Neuroscience department at the University of San Antonio recently, and was discussing my previous post, several people indicated to me that those interested in connectomes placed special emphasis on the cerebral cortex, apparently because those neurons are a little closer to the “interchangeable widget” end of the scale than other brain regions.

Losing the war - the ability of connectome theory to explain large parts of behaviour in many species - may not matter for Seung, however. For Seung, like many neuroscientists, there is only one battle worth fighting, the one for human minds. Near the end of the book, he writes:

(T)here is only one truly serious problem in science and technology, and that is immortality.

The last sections of the book deal with topics like transhumanism, immortality, and putting consciousness into computers. These are a very distinct group of pre-occupations, all revolving around human consciousness.

As a neurobiologist, I want a theory that can explain how nervous systems generate all the behaviours of all the diversity in the animal kingdom. A theory that only explains the human mind is a small and paltry thing.

Connectome theory reminds me of Anne Elk's theory:

In one sense, the theory is trivially true. But in another sense, the theory omits so much that it doesn't end up telling us anything we wanted to know.

* Seung uses an estimate that the human brain contains 100 billion neurons. More recent estimates put the count closer to 85 billion neurons, which he could not have had given the lead time of publishing a book.